protViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Documentation

The package ships with two pdf vignettes.

browseVignettes('protViz')

vignette('protViz')
vignette('PTM_MarkerFinder')

Installation

CRAN

install.packages('protViz')

from github

install the latest development version

install.packages('devtools')
library(devtools)
install_git('https://github.com/cpanse/protViz', build_vignettes = FALSE, quiet = FALSE)
library(protViz)

or

BiocManager::install('cpanse/protViz')

R CMD build hints

Rcpp::compileAttributes()

tools::package_native_routine_registration_skeleton(".", character_only = FALSE)


RcppExport SEXP _rcpp_module_boot_MyModule();

static const R_CallMethodDef CallEntries[] = {
    {"_rcpp_module_boot_MyModule", (DL_FUNC) &_rcpp_module_boot_MyModule, 0},
    {NULL, NULL, 0}
};

RcppExport void R_init_minModuleEx(DllInfo *dll) {
    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
    R_useDynamicSymbols(dll, FALSE);
}

Docker

docker pull cpanse/protviz \
&& docker run -d -p 8792:8787 cpanse/protviz     

connect to http://yourdockerhost:8791 using a web browser

• username: rstudio
• password: rstudio

Documentation

The package ships with a package vignette (browseVignettes(‘protViz’) and a reference manual (just type ?protViz on the R shell).

Both documents are also available on the package’s CRAN page.

Related approaches

• RforProteomics
• Spectra